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- EMDB-36933: Cryo-EM map of SV2A in complex with brivaracetam and BoNT/A2 Hc -
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Open data
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Basic information
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Title | Cryo-EM map of SV2A in complex with brivaracetam and BoNT/A2 Hc | |||||||||
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![]() | Synapse / epilepsy / antiepileptic drug / botulinum neurotoxin / MEMBRANE PROTEIN | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
![]() | Yamagata A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Authors: Atsushi Yamagata / Kaori Ito / Takehiro Suzuki / Naoshi Dohmae / Tohru Terada / Mikako Shirouzu / ![]() Abstract: More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. ...More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 H and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 H through protein-protein and protein-glycan interactions. LEV and BRV occupy the putative substrate-binding site in an outward-open conformation. A propyl group in BRV creates additional contacts with SV2A, explaining its higher binding affinity than that of LEV, which was further supported by label-free spectral shift assay. Numerous LEV derivatives have been developed as AEDs and positron emission tomography (PET) tracers for neuroimaging. Our work provides a structural framework for AEDs and BoNT recognition of SV2A and a blueprint for the rational design of additional AEDs and PET tracers. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 53.1 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 95.6 MB 95.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 864 KB | Display | ![]() |
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Full document | ![]() | 863.6 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36933_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36933_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Synaptic vesicle glycroprotein 2A in complex with brivaracetam an...
Entire | Name: Synaptic vesicle glycroprotein 2A in complex with brivaracetam and botulinum neurotoxin A2 Hc domain |
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Components |
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-Supramolecule #1: Synaptic vesicle glycroprotein 2A in complex with brivaracetam an...
Supramolecule | Name: Synaptic vesicle glycroprotein 2A in complex with brivaracetam and botulinum neurotoxin A2 Hc domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: Synaptic vesicle glycoprotein 2A
Supramolecule | Name: Synaptic vesicle glycoprotein 2A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Botulinum neurotoxin A2
Supramolecule | Name: Botulinum neurotoxin A2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Synaptic vesicle glycoprotein 2A
Macromolecule | Name: Synaptic vesicle glycoprotein 2A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDYKDDDDKE EGFRDRAAFI RGAKDIAKEV KKHAAKKVVK GLDRVQDEYS RRSYSRFEEE DDDDDFPAP SDGYYRGEGT QDEEEGGASS DATEGHDEDD EIYEGEYQGI PRAESGGKGE R MADGAPLA GVRGGLSDGE GPPGGRGEAQ RRKEREELAQ QYEAILRECG ...String: MDYKDDDDKE EGFRDRAAFI RGAKDIAKEV KKHAAKKVVK GLDRVQDEYS RRSYSRFEEE DDDDDFPAP SDGYYRGEGT QDEEEGGASS DATEGHDEDD EIYEGEYQGI PRAESGGKGE R MADGAPLA GVRGGLSDGE GPPGGRGEAQ RRKEREELAQ QYEAILRECG HGRFQWTLYF VL GLALMAD GVEVFVVGFV LPSAEKDMCL SDSNKGMLGL IVYLGMMVGA FLWGGLADRL GRR QCLLIS LSVNSVFAFF SSFVQGYGTF LFCRLLSGVG IGGSIPIVFS YFSEFLAQEK RGEH LSWLC MFWMIGGVYA AAMAWAIIPH YGWSFQMGSA YQFHSWRVFV LVCAFPSVFA IGALT TQPE SPRFFLENGK HDEAWMVLKQ VHDTNMRAKG HPERVFSVTH IKTIHQEDEL IEIQSD TGT WYQRWGVRAL SLGGQVWGNF LSCFGPEYRR ITLMMMGVWF TMSFSYYGLT VWFPDMI RH LQAVDYASRT KVFPGERVEH VTFNFTLENQ IHRGGQYFND KFIGLRLKSV SFEDSLFE E CYFEDVTSSN TFFRNCTFIN TVFYNTDLFE YKFVNSRLIN STFLHNKEGC PLDVTGTGE GAYMVYFVSF LGTLAVLPGN IVSALLMDKI GRLRMLAGSS VMSCVSCFFL SFGNSESAMI ALLCLFGGV SIASWNALDV LTVELYPSDK RTTAFGFLNA LCKLAAVLGI SIFTSFVGIT K AAPILFAS AALALGSSLA LKLPETRGQV LQ |
-Macromolecule #2: botulinum neurotoxin A2
Macromolecule | Name: botulinum neurotoxin A2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KNIVNTSILS IVYKKDDLID LSRYGAKINI GDRVYYDSID KNQIKLINLE SSTIEVILKN AIVYNSMYE NFSTSFWIKI PKYFSKINLN NEYTIINCIE NNSGWKVSLN YGEIIWTLQD N KQNIQRVV FKYSQMVNIS DYINRWIFVT ITNNRLTKSK IYINGRLIDQ ...String: KNIVNTSILS IVYKKDDLID LSRYGAKINI GDRVYYDSID KNQIKLINLE SSTIEVILKN AIVYNSMYE NFSTSFWIKI PKYFSKINLN NEYTIINCIE NNSGWKVSLN YGEIIWTLQD N KQNIQRVV FKYSQMVNIS DYINRWIFVT ITNNRLTKSK IYINGRLIDQ KPISNLGNIH AS NKIMFKL DGCRDPRRYI MIKYFNLFDK ELNEKEIKDL YDSQSNSGIL KDFWGNYLQY DKP YYMLNL FDPNKYVDVN NIGIRGYMYL KGPRGSVVTT NIYLNSTLYE GTKFIIKKYA SGNE DNIVR NNDRVYINVV VKNKEYRLAT NASQAGVEKI LSALEIPDVG NLSQVVVMKS KDDQG IRNK CKMNLQDNNG NDIGFIGFHL YDNIAKLVAS NWYNRQVGKA SRTFGCSWEF IPVDDG WGE SSL |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |